5UC3 | pdb_00005uc3

Structure of the dominant negative mutant Glucocorticoid Receptor alpha (L733K/N734P) complexed with RU-486

• PDB DOI: https://doi.org/10.2210/pdb5UC3/pdb

• Classification: HORMONE RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-12-21 Released: 2017-12-27 
• Deposition Author(s): Min, J., Cidlowski, J.A., Pedersen, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Nuclear receptor

Min, J., Pedersen, L.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.73 kDa 
• Atom Count: 4,023 
• Modeled Residue Count: 463 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor	A, B	257	Homo sapiens	Mutation(s): 2  Gene Names: NR3C1, GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
PHAROS:  P04150 GTEx:  ENSG00000113580

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
486	C [auth A], M [auth B]	11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE C29 H35 N O2 VKHAHZOOUSRJNA-GCNJZUOMSA-N
EPE	L [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MPD	D [auth A], E [auth A], N [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
486	BindingDB:  5UC3	Ki: min: 0.09, max: 169 (nM) from 18 assay(s)
		Kd: 15 (nM) from 1 assay(s)
		IC50: min: 8.00e-3, max: 33 (nM) from 34 assay(s)
		EC50: min: 0.6, max: 2500 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.749	α = 90
b = 88.32	β = 110.84
c = 64.672	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Min, J., Cidlowski, J.A., Pedersen, L.C.

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Structure summary
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary